Microbial Communities in Salt Marsh Systems and Their Responses to Anthropogenic Pollutants

  • Jonna M. CoombsEmail author
Part of the Advances in Environmental Microbiology book series (AEM, volume 6)


Salt marshes are vegetated terrestrial systems that develop along coastlines in temperate to arctic environments, in areas where surface or groundwater mixes with flooding from coastal tides. These environments perform essential ecosystem services such as storm buffering, carbon-trapping, and the protection of estuarine waters through the removal of land-based nutrients. The sediments in these environments are chemically complex, with gradients of salinity, redox, and pH that give rise to some of the most abundant and diverse microbial communities yet characterized. However, the significant loss of marsh surface area over the past 150 years has raised concerns about the stability of these microbial communities and their ability to deliver ecosystem services in the future. Many reasons have been proposed for the loss in marsh surface area, including anthropogenic pollutants, changes in predator and herbivore ecology, and global sea level rise. This chapter examines the structure of baseline microbial communities and their role in salt marsh biogeochemical cycling—and how anthropogenic land-based pollutants may negatively affect the ecosystem services provided by these microbial communities.


Salt marsh Nutrient cycling Heavy metals Sediment Microbial communities 


Compliance with Ethical Standards

Conflict of Interest

Jonna M. Coombs declares that she has no conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.


  1. Adams CA, Andrews JE, Jickells T (2012) Nitrous oxide and methane fluxes vs. carbon, nitrogen and phosphorous burial in new intertidal and salt marsh sediments. Sci Total Environ 434:240–251PubMedCrossRefPubMedCentralGoogle Scholar
  2. Agosta K (1985) The effect of tidally induced changes in the creek bank water table on pore water chemistry. Estuar Coast Shelf Sci 21:381–400CrossRefGoogle Scholar
  3. Almeida CMR, Mucha AP, Vasconcelos MTS (2004) Influence of the sea rush Juncus maritimus on metal concentration and speciation in estuarine sediment colonized by the plant. Environ Sci Technol 38:3112–3118PubMedCrossRefPubMedCentralGoogle Scholar
  4. An S, Gardiner WS (2002) Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link, versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay, Texas). Mar Ecol Prog Ser 237:41–50CrossRefGoogle Scholar
  5. Anderson IC, Tobias CR, Neikirk BB et al (1997) Development of a process-based nitrogen mass balance model for a Virginia (USA) Spartina alterniflora salt marsh: implications for net DIN flux. Mar Ecol Prog Ser 159:13–27CrossRefGoogle Scholar
  6. Andrades-Moreno L, del Castillo I, Parra R et al (2014) Prospecting metal-resistant plant-growth promoting rhizobacteria for rhizoremediation of metal contaminated estuaries using Spartina densiflora. Environ Sci Pollut Res 21:3713–3721CrossRefGoogle Scholar
  7. Anisfeld SC, Hill TD (2012) Fertilization effects on elevation change and belowground carbon balance in a Long Island Sound tidal marsh. Estuar Coast 35:201–211CrossRefGoogle Scholar
  8. Anjum NA, Ahmad I, Válega M et al (2014) Salt marsh halophyte services to metal-metalloid remediation: assessment of the process and underlying mechanisms. Crit Rev Environ Sci Technol 44:2038–2016. CrossRefGoogle Scholar
  9. Ansede JH, Friedman R, Yoch DC (2001) Phylogenetic analysis of culturable dimethyl sulfide-producing bacteria from a Spartina-dominated salt marsh and estuarine water. Appl Environ Microbiol 67:1210–1217PubMedPubMedCentralCrossRefGoogle Scholar
  10. Aziz SAA, Nedwell DB (1986) The nitrogen cycle of an East Coast, U.K. saltmarsh: II. Nitrogen fixation, nitrification, denitrification, tidal exchange. Estuar Coast Shelf Sci 22:689–704CrossRefGoogle Scholar
  11. Bagwell CE, Lovell CR (2000) Microdiversity of culturable diazotrophs from the rhizoplanes of the salt marsh grasses Spartina alterniflora and Juncus roemerianus. Microb Ecol 39:128–136PubMedCrossRefPubMedCentralGoogle Scholar
  12. Bagwell CE, Piceno YM, Ashburne-Lucas A et al (1998) Physiological diversity of the rhizosphere diazotroph assemblages of selected salt marsh grasses. Appl Environ Microbiol 64:4276–4282PubMedPubMedCentralGoogle Scholar
  13. Bagwell CE, Dantzler M, Bergholz PW et al (2001) Host-specific ecotype diversity of rhizoplane diazotrophs of the perennial glasswort Salicornia virginica and selected salt marsh grasses. Aquat Microb Ecol 23:293–300CrossRefGoogle Scholar
  14. Bahr M, Crump BC, Klepac-Ceraj V et al (2005) Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ Microbiol 7:1175–1185PubMedCrossRefPubMedCentralGoogle Scholar
  15. Bañeras L, Ruiz-Rueda O, López-Flores R et al (2012) The role of plant type and salinity in the selection for the denitrifying community structure in the rhizosphere of wetland vegetation. Int Microbiol 15:89–99PubMedPubMedCentralGoogle Scholar
  16. Barbier EB, Hacker SD, Kennedy C et al (2011) The value of estuarine and coastal ecosystem services. Ecol Monogr 81:169–193CrossRefGoogle Scholar
  17. Batty LC, Baker AJM, Wheeler BD et al (2000) The effect of pH and plaque on the uptake of Cu and Mn in Phragmites australis(Cav.) Trin ex. Steudel. Ann Bot 86:647–653CrossRefGoogle Scholar
  18. Bergholz PW, Bagwell CE, Lovell CR (2001) Physiological diversity of rhizoplane diazotrophs of the saltmeadow cordgrass Spartina patens: implications for host specific ecotypes. Microb Ecol 42:466–473PubMedCrossRefPubMedCentralGoogle Scholar
  19. Bernhard AE, Bollmann A (2010) Estuarine nitrifiers: new players, patterns and processes. Estuar Coast Shelf Sci 88:1–11CrossRefGoogle Scholar
  20. Bernhard AE, Donn T, Giblin AE et al (2005) Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system. Environ Microbiol 7:1289–1297PubMedCrossRefPubMedCentralGoogle Scholar
  21. Bernhard AE, Dwyer C, Idrizi A et al (2015) Long-term impacts of disturbance on nitrogen-cycling bacteria in a New England salt marsh. Front Microbiol 6:46. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Bertness MD (1991) Zonation of Spartina patens and Spartina alterniflora in a New England salt marsh. Ecology 72:138–148CrossRefGoogle Scholar
  23. Bertness MD, Ewanchuk PJ, Silliman BR (2002) Anthropogenic modification of New England salt marsh landscapes. PNAS 99:1395–1398PubMedCrossRefPubMedCentralGoogle Scholar
  24. Bertness MD, Brisson CP, Coverdale TC et al (2014) Experimental predator removal causes rapid salt marsh die-off. Ecol Lett 17:830–845PubMedPubMedCentralCrossRefGoogle Scholar
  25. Best EPH, Hintelmann H, Dimock B et al (2008) Natural cycles and transfer of mercury through coastal marsh vegetation dominated by Spartina foliosa and Salicornia virginica. Estuar Coasts 31:1072–1088CrossRefGoogle Scholar
  26. Bharathkumar S, Paul D, Nair S (2008) Microbial diversity of culturable heterotrophs in the rhizosphere of salt marsh grass Porteresia coarctata (Tateoka) in a mangrove ecosystem. J Basic Microbiol 48:10–15PubMedCrossRefPubMedCentralGoogle Scholar
  27. Blum LK, Davey E (2013) Below the salt marsh surface: visualization of plant roots by computer-aided tomography. Oceanography 26:85–87CrossRefGoogle Scholar
  28. Blum LK, Roberts MS, Garland JL et al (2004) Distribution of microbial communities associated with the dominant high marsh plants and sediments of the United States east coast. Microb Ecol 48:375–388PubMedCrossRefPubMedCentralGoogle Scholar
  29. Bowen JL, Crump BC, Deegan LA et al (2009) Salt marsh bacteria: their distribution and response to external nutrient inputs. ISME J 3:924–934PubMedCrossRefPubMedCentralGoogle Scholar
  30. Bowen JL, Ward BB, Morrison HG et al (2011) Microbial community composition in sediments resists perturbation by nutrient enrichment. ISME J 5:1540–1548PubMedPubMedCentralCrossRefGoogle Scholar
  31. Bowen JL, Morrison HG, Hobbie JE et al (2012) Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates. ISME J 6:2014–2023PubMedPubMedCentralCrossRefGoogle Scholar
  32. Bowen JL, Byrnes JEK, Weisman D et al (2013) Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments. Front Microbiol 4:342. CrossRefPubMedPubMedCentralGoogle Scholar
  33. Boyer KE, Zedler JB (1999) Nitrogen addition could shift plant community composition in a restored California salt marsh. Restor Ecol 7:74–85CrossRefGoogle Scholar
  34. Brin LD, Valeila I, Goehringer D et al (2010) Nitrogen interception and export by experimental salt marsh plots exposed to chronic nutrient addition. Mar Ecol Prog Ser 400:3–17CrossRefGoogle Scholar
  35. Brownstein G, Bastow Wilson J, Burritt DJ (2013) Waterlogging tolerance on a New Zealand salt marsh. J Exp Mar Biol Ecol 446:202–208CrossRefGoogle Scholar
  36. Buresh RJ, DeLaune RD, Patrick WH Jr (1980) Nitrogen and phosphorous distribution and utilization by Spartina alterniflora in a Louisiana Gulf Coast marsh. Estuaries 3:111–121CrossRefGoogle Scholar
  37. Burgin AJ, Hamilton SK (2007) Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Front Ecol Environ 5:89–96CrossRefGoogle Scholar
  38. Burke DJ, Hamerlynck EP, Hahn D (2002a) Effect of arbuscular mycorrhizae on soil microbial populations and associated plant performance of the salt marsh grass Spartina patens. Plant Soil 239:141–154CrossRefGoogle Scholar
  39. Burke DJ, Hamerlynck EP, Hahn D (2002b) Interactions among plant species and microorganisms in salt marsh sediments. Appl Environ Microbiol 68:1157–1164PubMedPubMedCentralCrossRefGoogle Scholar
  40. Burke DJ, Hamerlynck EP, Hahn D (2003) Interactions between the salt marsh grass Spartina patens, arbuscular mycorrhizal fungi and sediment bacteria during the growing season. Soil Biol Biochem 35:501–511CrossRefGoogle Scholar
  41. Caçador I, Vale C, Catarino F (1996) Accumulation of Zn, Pb, Cu, Cr and Ni in sediments between roots of the Targus Estuary salt marshes, Portugal. Estuar Coast Shelf Sci 42:393–403CrossRefGoogle Scholar
  42. Caçador I, Vale C, Catarino F (2000) Seasonal variation of Zn, Pb, Cu and Cd concentrations in the root-sediment system of Spartina maritima and Halimione portulacoides from Tagus estuary salt marshes. Mar Environ Res 49:279–290PubMedCrossRefPubMedCentralGoogle Scholar
  43. Caçador I, Caetano M, Duarte B et al (2009) Stock and losses of trace metals from salt marsh plants. Mar Environ Res 67:75–82PubMedCrossRefPubMedCentralGoogle Scholar
  44. Caffrey JM, Murrell MC, Wigand C et al (2007) Effect of nutrient loading on biogeochemical and microbial processes in a New England salt marsh. Biogeochemistry 82:251–264CrossRefGoogle Scholar
  45. Calado ML, Barata M (2012) Salt marsh fungi. In: Jones EBG, Pang K-L (eds) Marine fungi and fungal-like organisms. De Gruyter, BerlinGoogle Scholar
  46. Calaldo ML, Carvalho L, Pang K-L et al (2015) Diversity and ecological characterization of sporulating higher filamentous marine fungi associated with Spartina maritima (Curtis) Fernald in two Portugese salt marshes. Microb Ecol 70:612–633CrossRefGoogle Scholar
  47. Canário J, Caetano M, Vale C et al (2007) Evidence for elevated production of methylmercury in salt marshes. Environ Sci Technol 41:7376–7382PubMedCrossRefPubMedCentralGoogle Scholar
  48. Cao Y, Cherr GN, Córdova-Kreylos AL et al (2006) Relationship between sediment microbial communities and pollutants in two California salt marshes. Microbiol Ecol 52:619–633CrossRefGoogle Scholar
  49. Cao Y, Green PG, Holden PA (2008) Microbial community composition and denitrifiying enzyme activities in salt marsh sediments. Appl Environ Microbiol 74:7585–7595PubMedPubMedCentralCrossRefGoogle Scholar
  50. Capone DG, Reese DD, Kiene RP (1983) Effects of metals on methanogenesis, sulfate reduction, carbon dioxide evolution and microbial biomass in anoxic marsh sediments. Appl Environ Microbiol 45:1586–1591PubMedPubMedCentralGoogle Scholar
  51. Carrasco L, Caravaca F, Álvarez-Rogel J et al (2006) Microbial processes in the rhizosphere of a heavy metals-contaminated Mediterranean salt marsh: a facilitating role of AM fungi. Chemosphere 64:104–111PubMedCrossRefPubMedCentralGoogle Scholar
  52. Cartaxana P, Caçador I, Vale C et al (1999) Seasonal variation of inorganic nitrogen and net mineralization in a salt marsh ecosystem. Mangrove Salt Marshes 3:127–134CrossRefGoogle Scholar
  53. Chai M, Shi F, Li R et al (2014) Heavy metal contamination and ecological risk in Spartina alterniflora marsh in intertidal sediments of Bohui Bay, China. Mar Pollut Bull 84:115–124PubMedCrossRefPubMedCentralGoogle Scholar
  54. Chaudhury DR, Gautam RK, Yousuf B et al (2015) Nutrients, microbial community structure and functional gene abundance of rhizosphere and bulk soils of halophytes. Appl Soil Ecol 91:16–26CrossRefGoogle Scholar
  55. Chen Y, Chen G, Ye Y (2015) Coastal vegetation invasion increases greenhouse gas emission from wetland soil but also increases soil carbon accumulation. Sci Total Environ 526:19–28PubMedCrossRefPubMedCentralGoogle Scholar
  56. Cleary DFR, Oliveira V, Gomes NCM et al (2012) Impact of sampling depth and plant species on local environmental conditions, microbiological parameters and bacterial composition in a mercury contaminated salt marsh. Mar Pollut Bull 64:263–271PubMedCrossRefPubMedCentralGoogle Scholar
  57. Cloern JE (2001) Our evolving conceptual model of the coastal eutrophication problem. Mar Ecol Prog Ser 210:223–253CrossRefGoogle Scholar
  58. Costa AL, Carolino M, Caçador I (2007) Microbial activity profiles in Tagus estuary salt marsh sediments. Hydrobiologia 587:169–175CrossRefGoogle Scholar
  59. Dale OR, Tobias CR, Song B (2009) Biogeographical distribution of diverse anaerobic ammonium oxidizing (anammox) bacteria in Cape Fear River Estuary. Environ Microbiol 11:1194–1207PubMedCrossRefPubMedCentralGoogle Scholar
  60. Darby FA, Turner E (2008) Effects of eutrophication on salt marsh root and rhizome biomass accumulation. Mar Ecol Prog Ser 363:63–70CrossRefGoogle Scholar
  61. Darjany LE, Whitcraft CR, Dillon JG (2014) Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing. Front Microbiol 5:263. CrossRefPubMedPubMedCentralGoogle Scholar
  62. Davis DA, Gamble MD, Bagwell CE et al (2011) Responses of salt marsh plant rhizosphere diazotroph assemblages to changes in marsh elevation, edaphic conditions and plant host species. Microb Ecol 61:386–398PubMedCrossRefPubMedCentralGoogle Scholar
  63. Deegan LA, Johnson DS, Warren RS et al (2012) Coastal eutrophication as a driver of salt marsh loss. Nature 490:388–392PubMedCrossRefPubMedCentralGoogle Scholar
  64. DeLaune RD, Smith CJ (1985) Release of nutrients and metals following oxidation of freshwater and saline sediment. J Environ Qual 14:164–168CrossRefGoogle Scholar
  65. DeLaune RD, Smith CJ, Patrick WHJ (1983) Nitrogen losses from a Louisiana Gulf coast salt marsh. Estuar Coast Shelf Sci 17:133–141CrossRefGoogle Scholar
  66. Deng Y-J, Wang SY (2016) Synergistic growth in bacteria depends on substrate complexity. J Microbiol 54:23–30PubMedPubMedCentralCrossRefGoogle Scholar
  67. Dicker HJ, Smith DW (1980) Enumeration and relative importance of acetylene-reducing (nitrogen-fixing) bacteria in a Delaware salt marsh. Appl Environ Microbiol 39:1019–1025PubMedPubMedCentralGoogle Scholar
  68. Dong LF, Smith CJ, Papaspyrou S et al (2009) Changes in bethic denitrification, nitrate ammonification, and anammox process rates and nitrate and nitrite reductase gene abundances along an estuarine nutrient gradient (the Colne Estuary, United Kingdom). Appl Environ Microbiol 75:3171–3179PubMedPubMedCentralCrossRefGoogle Scholar
  69. Doyle MO, Otte ML (1997) Organism-induced accumulation of iron, zinc and arsenic in wetland soils. Environ Pollut 96:1–11PubMedCrossRefPubMedCentralGoogle Scholar
  70. Duarte B, Reboreda R, Caçador I (2008a) Seasonal variation of extracellular enzyme activity (EEA) and its influence on metal speciation in a polluted salt marsh. Chemosphere 73:1056–1063PubMedCrossRefPubMedCentralGoogle Scholar
  71. Duarte CM, Dennison WC, Orth RJW et al (2008b) The charisma of coastal ecosystems: addressing the imbalance. Estuar Coasts 31:233–238CrossRefGoogle Scholar
  72. Duarte B, Almeida PR, Caçador I (2009) Spartima maritima (cordgrass) rhizosediment extracellular enzyme activity and its role in organic matter decomposition processes and metal speciation. Mar Ecol 30(Suppl. 1):65–73CrossRefGoogle Scholar
  73. Edgcomb VP, McDonald JH, Devereux R et al (1999) Estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16S Ribosomal DNA. Appl Environ Microbiol 65:1516–1523PubMedPubMedCentralGoogle Scholar
  74. Emery NC, Ewanchuk PJ, Bertness MD (2001) Competition and salt-marsh plant zonation: stress tolerators may be dominant competitors. Ecology 82:2471–2485CrossRefGoogle Scholar
  75. Fox L, Valeila I, Kinney EL (2012) Vegetation cover and elevation in long-term experimental nutrient-enrichment plots in Great Sippewissett Salt Marsh, Cape Cod, Massachusetts: implications for eutrophication and sea level rise. Estuar Coasts 35:445–458CrossRefGoogle Scholar
  76. Franklin RB, Blum LK, McComb AC et al (2002) A geostatistical analysis of small-scale variability in bacterial abundance and community structure in salt marsh creek bank sediments. FEMS Microbiol Ecol 42:71–80PubMedCrossRefPubMedCentralGoogle Scholar
  77. Freitag TE, Chang L, Prosser JI (2006) Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient. Environ Microbiol 8:684–696PubMedCrossRefPubMedCentralGoogle Scholar
  78. Friedrich CG, Rother D, Bardischewsky F et al (2001) Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism? Appl Environ Microbiol 67:2873–2882PubMedPubMedCentralCrossRefGoogle Scholar
  79. Galloway JN, Townsend AR, Erisman JW et al (2008) Transformation of the nitrogen cycle: recent trends, questions and potential solutions. Science 320:889–892PubMedCrossRefPubMedCentralGoogle Scholar
  80. Gamble MD, Bagwell CE, LaRocque J et al (2010) Seasonal variability of diazotroph assemblages associated with the rhizosphere of the salt marsh cordgrass, Spartina alterniflora. Microb Ecol 59:253–265PubMedCrossRefPubMedCentralGoogle Scholar
  81. Gandy EL, Yoch DC (1988) Relationship between nitrogen-fixing sulfate reducers and fermenters in salt marsh sediments and roots of Spartina alterniflora. Appl Environ Microbiol 54:2031–2036PubMedPubMedCentralGoogle Scholar
  82. Gedan KB, Silliman BR, Berness MD (2009) Centuries of human-driven change in salt marsh ecosystems. Annu Rev Mar Sci 1:117–141CrossRefGoogle Scholar
  83. Giblin AE, Wieder RK (1992) Sulphur cycling in marine and freshwater wetlands. In: Howarth RW, Stewart JWB, Ivanov MV (eds) Sulphur cycling on the continents. Wiley, New YorkGoogle Scholar
  84. Giblin AE, Bourg A, Valeila I et al (1980) Uptake and losses of heavy metals in sewage sludge by a New England salt marsh. Am J Bot 67:1059–1068CrossRefGoogle Scholar
  85. Giblin AE, Tobias CR, Song B et al (2013) The importance of dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen cycle of coastal ecosystems. Oceanography 26:124–131CrossRefGoogle Scholar
  86. Goßner AS, Küsel K, Schulz D et al (2006) Trophic interaction of the aerotolerant anaerobe Clostridium intestinale and the acetogen Sporomusa rhizae sp. nov. isolated from the roots of the black needlerush Juncus roemerianus. Microbiology 152:1209–1219PubMedCrossRefPubMedCentralGoogle Scholar
  87. Hamersley MR, Howes BL (2005) Coupled nitrification-denitrification measured in situ in a Spartina alterniflora marsh with a 15NH4 + tracer. Mar Ecol Prog Ser 299:123–135CrossRefGoogle Scholar
  88. Hatzenpichler R, Lebedeva EV, Spieck E et al (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. PNAS 105:2134–2139PubMedCrossRefPubMedCentralGoogle Scholar
  89. Hewson I, Jacobson Meyers ME, Fuhrman JA (2007) Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands. Environ Microbiol 9:923–933PubMedCrossRefPubMedCentralGoogle Scholar
  90. Hines ME, Lyons WB, Armstrong PB et al (1984) Seasonal metal remobilization in the sediments of Great Bay, New Hampshire. Mar Chem 15:173–187CrossRefGoogle Scholar
  91. Hines ME, Knollmeyer S, Tugel JB (1989) Sulfate reduction and other sedimentary biogeochemistry in a northern New England salt marsh. Limnol Oceanogr 34:578–590CrossRefGoogle Scholar
  92. Hines ME, Evans RS, Sharak Genthner BR et al (1999) Molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of Spartina alterniflora. Appl Environ Microbiol 65:2209–2216PubMedPubMedCentralGoogle Scholar
  93. Hong Y, Liao D, Hu A et al (2015) Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing. Can J Microbiol 61:723–733PubMedCrossRefPubMedCentralGoogle Scholar
  94. Hopkinson CS, Giblin AE (2008) Nitrogen dynamics of coastal salt marshes. In: Nitrogen in the marine environment. Elsevier, Amsterdam, pp 991–1025CrossRefGoogle Scholar
  95. Horner-Devine CM, Lage M, Hughes JB et al (2004) A taxa-area relationship for bacteria. Nature 432:750–753PubMedCrossRefPubMedCentralGoogle Scholar
  96. Howarth RW (1984) The ecological significance of sulfur in the energy dynamics of salt marsh and coastal marine sediments. Biogeochemistry 1:5–27CrossRefGoogle Scholar
  97. Howarth RW (1993) Microbial processes in salt marsh sediments. In: Ford TE (ed) Aquatic microbiology: an ecological approach. Blackwell Scientific Publishing, OxfordGoogle Scholar
  98. Howarth RW (2008) Coastal nitrogen pollution: a review of sources and trends globally and regionally. Harmful Algae 8:14–20CrossRefGoogle Scholar
  99. Howarth RW, Giblin A (1983) Sulfate reduction in the salt marshes of Sapelo Island, Georgia. Limnol Oceanogr 28:70–82CrossRefGoogle Scholar
  100. Howarth RW, Hobbie JE (1982) The regulation of decomposition and heterotrophic microbial activity in salt marsh soils: a review. In: Kennedy VS (ed) Estuarine comparisons. Academic Press, New York, pp 183–207CrossRefGoogle Scholar
  101. Howarth RW, Teal JM (1979) Sulfate reduction in a New England salt marsh. Limnol Oceanogr 24:999–1013CrossRefGoogle Scholar
  102. Howes BL, Teal JM (1994) Oxygen loss from Spartina alterniflora and its relationship to salt marsh oxygen balance. Oecologia 97:431–438Google Scholar
  103. Howarth RW, Anderson J, Cloern C et al (2000) Nutrient pollution of coastal rivers, bays and seas. Issues Ecol 7:1–15Google Scholar
  104. Irvine IC, Vivanco L, Bentley PN et al (2012) The effect of nitrogen enrichment on C1-cycling microorganisms and methane flux in salt marsh sediments. Front Microbiol 3:90. CrossRefPubMedPubMedCentralGoogle Scholar
  105. Jones CM, Hallin S (2010) Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. ISME J 4:633–641PubMedCrossRefPubMedCentralGoogle Scholar
  106. Jones WJ, Paynter MJB (1980) Populations of methane-producing bacteria and in vitro methanogenesis in salt marsh and estuary sediments. Appl Environ Microbiol 39:864–871PubMedPubMedCentralGoogle Scholar
  107. Jones CM, Stres B, Rosenquist M et al (2008) Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol 25:1955–1966PubMedCrossRefPubMedCentralGoogle Scholar
  108. Joye SB, Hollibaugh JT (1995) Influence of sulfide inhibition of nitrification on nitrogen regeneration in sediments. Science 270:623–625CrossRefGoogle Scholar
  109. Kappler U, Dahl C (2001) Enzymology and molecular biology of prokaryotic sulfite oxidation. FEMS Microbiol Lett 203:1–9PubMedCrossRefPubMedCentralGoogle Scholar
  110. Kearns PJ, Angell JH III, Feinman SG et al (2015) Long-term nutrient addition differentially alters community composition and diversity of genes that control nitrous oxide flux from salt marsh sediments. Estuar Coast Shelf Sci 154:39–47CrossRefGoogle Scholar
  111. Keith-Roach MJ, Day JP, Fifield LK et al (2000) Seasonal variations in interstitial water transuranium element concentrations. Environ Sci Technol 34:4273–4277CrossRefGoogle Scholar
  112. Keith-Roach MJ, Bryan ND, Bardgett RD et al (2002) Seasonal changes in the microbial community of a salt marsh, measured by phospholipid fatty acid analysis. Biogeochemistry 60:77–96CrossRefGoogle Scholar
  113. Kelly DP, Shergill JK, Lu WP et al (1997) Oxidative metabolism of inorganic sulfur compounds by bacteria. Antonie Van Leeuwenhoek 71:95–107PubMedCrossRefPubMedCentralGoogle Scholar
  114. Kerner M (1993) Coupling of microbial fermentation and respiration processes in an intertidal mud flat of the Elbe Estuary. Limnol Oceanogr 38:314–330CrossRefGoogle Scholar
  115. Khalid RA, Patrick WHJ, Gambrell RP (1978) Effect of dissolved oxygen on chemical transformations of heavy metals, phosphorous, and nitrogen in an estuarine sediment. Estuar Coast Mar Sci 6:21–35CrossRefGoogle Scholar
  116. Kiehl K, Esselink P, Bakker JP (1997) Nutrient limitation and plant species composition in temperate salt marshes. Oecologia 111:325–330PubMedCrossRefPubMedCentralGoogle Scholar
  117. King GM, Garey MA (1999) Ferric iron reduction by bacteria associated with the roots of freshwater and marine macrophytes. Appl Environ Microbiol 65:4393–4398PubMedPubMedCentralGoogle Scholar
  118. King GM, Wiebe WJ (1978) Methane release from soils of a Georgia salt marsh. Geochim Cosmochim Acta 42:343–348CrossRefGoogle Scholar
  119. King GM, Wiebe WJ (1980) Tracer analysis of methanogenesis in salt marsh soils. Appl Environ Microbiol 39:877–881PubMedPubMedCentralGoogle Scholar
  120. Kinney EL, Valiela I (2013) Changes in δ15N in salt marsh sediments in a long-term fertilization study. Mar Ecol Prog Ser 477:41–52CrossRefGoogle Scholar
  121. Kirwan ML, Gutenspergen GR (2012) Feedbacks between inundation, root production, and shoot growth in a rapidly submerging brackish marsh. J Ecol 100:764–770CrossRefGoogle Scholar
  122. Kirwan ML, Megonigal JP (2013) Tidal wetland stability in the face of human impacts and sea-level rise. Nature 504:53–60PubMedCrossRefPubMedCentralGoogle Scholar
  123. Klepac-Ceraj V, Bahr M, Crump BC et al (2004) High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environ Microbiol 6:686–698PubMedCrossRefPubMedCentralGoogle Scholar
  124. Könneke M, Bernhard AE, de la Torre JR et al (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546PubMedCrossRefGoogle Scholar
  125. Koop-Jakobsen K, Giblin AE (2010) The effect of increased nitrate loading on nitrate reduction via denitrification and DNRA in salt marsh sediments. Limnol Oceanogr 55:789–802CrossRefGoogle Scholar
  126. Koretsky CM, Van Cappellan P, DiChristina TJ et al (2005) Salt marsh pore water chemistry does not correlate with microbial community structure. Estuar Coast Shelf Sci 62:233–251CrossRefGoogle Scholar
  127. Kostka JE, Roychoudhury A, Van Cappellen P (2002) Rates and controls of anaerobic microbial respiration across spatial and temporal gradients in saltmarsh sediments. Biogeochemistry 60:49–76CrossRefGoogle Scholar
  128. Kristensen E, Kostka JE (2005) Macrofaunal burrows and irrigation in marine sediment: microbiological and biogeochemical interactions. In: Kristensen E, Kostka JE, Haese R (eds) Interactions between macro- and micro-organisms in marine sediments. American Geophysical Union, Washington, DCCrossRefGoogle Scholar
  129. Kuehn KA, Lemke MJ, Suberkropp K et al (2000) Microbial biomass and production associated with decaying leaf litter of the emergent macrophyte Juncus effusus. Limnol Oceanogr 45:862–870CrossRefGoogle Scholar
  130. Langley JA, Megonigal JP (2010) Ecosystem response to elevated CO2 levels limited by nitrogen-induced plant species shift. Nature 466:96–99PubMedCrossRefPubMedCentralGoogle Scholar
  131. Leaphart AB, Lovell CR (2001) Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria. Appl Environ Microbiol 67:1392–1395PubMedPubMedCentralCrossRefGoogle Scholar
  132. Leaphart AB, Friez MJ, Lovell CR (2003) Formyltetrahydrofolate synthetase sequences from salt marsh plant foots reveal a diversity of acetogenic bacteria and other bacterial functional groups. Appl Environ Microbiol 69:693–696PubMedPubMedCentralCrossRefGoogle Scholar
  133. Lever MA (2011) Acetogenesis in the energy-starved deep-biosphere—a paradox? Front Microbiol 2:284. CrossRefPubMedPubMedCentralGoogle Scholar
  134. Levine JM, Hacker SD, Harley CDG et al (1998) Nitrogen effects on an interaction chain in a salt marsh community. Oecologia 117:266–272PubMedCrossRefPubMedCentralGoogle Scholar
  135. Lin H, Taillefert M (2014) Key geochemical factors regulating Mn(IV)-catalyzed anaerobic nitrification in coastal marine sediments. Geochim Cosmochim Acta 133:17–33CrossRefGoogle Scholar
  136. Lindau CW, DeLaune RD (1991) Dinitrogen and nitrous oxide emission and entrapment in Spartina alterniflora saltmarsh soils following addition of N-15 labelled ammonium and nitrate. Estuar Coast Shelf Sci 32:161–172CrossRefGoogle Scholar
  137. Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125:171–189PubMedCrossRefPubMedCentralGoogle Scholar
  138. Lovell CR, Davis DA (2012) Specificity of salt marsh diazotrophs from vegetation zones and plant hosts: results from a North American marsh. Front Microbiol 3:84. CrossRefPubMedPubMedCentralGoogle Scholar
  139. Lovell CR, Bagwell CE, Czákó M et al (2001) Stability of a rhizosphere microbial community exposed to natural and manipulated environmental variability. FEMS Microbiol Ecol 38:69–76CrossRefGoogle Scholar
  140. Lovell CR, Decker PV, Bagwell CE et al (2008) Analysis of a diverse assemblage of diazotrophic bacteria from Spartina alterniflora using DGGE and clone library screening. J Microbiol Methods 73:160–171PubMedCrossRefPubMedCentralGoogle Scholar
  141. Lovley DR (1997) Microbial Fe (III) reduction in subsurface environments. FEMS Microbiol Rev 20:305–313CrossRefGoogle Scholar
  142. Lowe KL, Dichristina TJ (2000) Microbiological and geochemical characterization of microbial Fe(III) reduction in salt marsh sediments. Geomicrobiol J 17:163–178CrossRefGoogle Scholar
  143. Luther GW III, Kostka JE, Church TM (1992) Seasonal iron cycling in the salt-marsh sedimentary environment: the importance of ligand complexes with Fe(II) and Fe(III) in the dissolution of Fe(III) minerals and pyrite, respectively. Mar Chem 40:81–103CrossRefGoogle Scholar
  144. Lydell C, Dowell L, Sikaroodi M et al (2004) A population survey of members of the phylum Bacteriodetes isolated from salt marsh sediments along the East Coast of the United States. Microb Ecol 48:263–273PubMedCrossRefPubMedCentralGoogle Scholar
  145. Ma H, Aelion M (2005) Ammonium production during microbial nitrate removal in soil microcosms from a developing marsh estuary. Soil Biol Biochem 37:1869–1878CrossRefGoogle Scholar
  146. Machado A, Magalhães C, Mucha AP et al (2012) Microbial communities within salt marsh sediments: composition, abundance and pollution constraints. Estuar Coast Shelf Sci 99:145–152CrossRefGoogle Scholar
  147. Maia LB, Moura JG (2014) How biology handles Nitrite. Chem Rev 114:5273–5357PubMedCrossRefPubMedCentralGoogle Scholar
  148. Maltby E (1988) Global wetlands—history, current status and future. In: Hook DD (ed) The ecology and management of wetlands. Timber Press, Portland, pp 3–14Google Scholar
  149. Marques B, Lillebø AI, Pereira E et al (2011) Mercury cycling and sequestration in salt marshes sediments: an ecosystem service provided by Juncus maritimus and Scirpus maritimus. Environ Pollut 159:1869–1876PubMedCrossRefPubMedCentralGoogle Scholar
  150. McClung CR, van Berkum P, Davis RE et al (1983) Enumeration and localization of N2-fixing bacteria associated with the roots of Spartina alterniflora Loisel. Appl Environ Microbiol 45:1914–1920PubMedPubMedCentralGoogle Scholar
  151. Mesa J, Mateos-Naranjo E, Caviedes MA et al (2015) Endophytic cultivable bacteria of the metal bioaccumulator Spartina maritime improve plant growth but not metals uptake in polluted marshes soils. Front Microbiol 6:1450. CrossRefPubMedPubMedCentralGoogle Scholar
  152. Middleburg JJ, Nieuwenhuize J, Lubberts RK et al (1997) Organic carbon isotope systematics of coastal marshes. Estuar Coast Shelf Sci 45:681–687CrossRefGoogle Scholar
  153. Mitsch WJ, Gosselink JG (2007) Wetlands, 4th edn. Wiley, Hoboken, NJGoogle Scholar
  154. Mohan SB, Schmid M, Jetten M et al (2004) Detection and widespread distribution of the nrfA gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. FEMS Microbiol Ecol 49:433–443PubMedCrossRefPubMedCentralGoogle Scholar
  155. Morozkina EV, Zvyagilskaya RA (2007) Nitrate reductases: structure, functions and effect of stress factors. Biochem Mosc 72:1151–1160CrossRefGoogle Scholar
  156. Morris JT, Bradley PM (1999) Effects of nutrient loading on the carbon balance of coastal wetland sediments. Limnol Oceanogr 44:699–702CrossRefGoogle Scholar
  157. Morris JT, Sundareshwar PV, Nietch CT et al (2002) Responses of coastal wetlands to rising sea level. Ecology 83:2869–2877CrossRefGoogle Scholar
  158. Morris JT, Sundberg K, Hopkinson CS (2013) Salt marsh primary productivity and its responses to relative sea level and nutrients in estuaries at Plum Island, Massachusetts, and North Inlet, South Carolina, USA. Oceanography 26:78–84CrossRefGoogle Scholar
  159. Moseman-Valtierra SM, Armaiz-Nolla K, Levin LA (2010) Wetland response to sedimentation and nitrogen loading: diversification and inhibition of nitrogen-fixing microbes. Ecol Appl 20:1556–1568PubMedCrossRefPubMedCentralGoogle Scholar
  160. Mucha AP, Almeida CMR, Megalhães CM et al (2011) Salt marsh plant-microorganism interaction in the presence of mixed contamination. Int Biodeter Biodegr 65:326–333CrossRefGoogle Scholar
  161. Nellemann C, Corcoran E, Duarte CM, et al. (2009) Blue Carbon: the role of healthy oceans in binding carbon, a rapid response assessment. United Nations Environment Programme, GRID-Arendal,
  162. Nelson KA, Moin NS, Bernhard AE (2009) Archael diversity and the prevalence of Crenarchaeota in salt marsh sediments. Appl Environ Microbiol 75:4211–4215PubMedPubMedCentralCrossRefGoogle Scholar
  163. Newton C, Thornber C (2013) Ecological impacts of macroalgal blooms on salt marsh communities. Estuar Coasts 36:365–376CrossRefGoogle Scholar
  164. Oczkowski A, Wigand C, Hanson A et al (2015) Nitrogen retention in salt marsh systems across nutrient-enrichment, elevation and precipitation regimes: a multiple-stressor experiment. Estuar Coasts 39:68–81. CrossRefGoogle Scholar
  165. Oliveira V, Santos AL, Aguiar C et al (2012) Prokaryotes in salt marsh sediments of Ria de Aveiro: effects of halophyte vegetation on abundance and diversity. Estuar Coast Shelf Sci 110:61–68CrossRefGoogle Scholar
  166. Oremland RS, Polcin S (1982) Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in estuarine sediments. Appl Environ Microbiol 44:1270–1276PubMedPubMedCentralGoogle Scholar
  167. Otero XL, Macías F (2002) Spatial and seasonal variation in heavy metals in interstitial water of salt marsh soils. Environ Pollut 120:183–190PubMedCrossRefPubMedCentralGoogle Scholar
  168. Otte ML, Rozema J, Koster L et al (1989) Iron plaque on roots of Aster tripolium L.: interaction with zinc uptake. New Phytol 111:309–317CrossRefGoogle Scholar
  169. Patriquin DG, McClung CR (1978) Nitrogen accretion, and the nature and possible significance of N2 fixation (acetylene reduction) in a Nova Scotian Spartina alterniflora stand. Mar Biol 47:227–242CrossRefGoogle Scholar
  170. Pendleton L, Donato DC, Murray BC et al (2012) Estimating global “blue carbon” emissions from conversion and degradation of vegetated coastal ecosystems. PLoS One 7(9):e43542. CrossRefPubMedPubMedCentralGoogle Scholar
  171. Peng X, Yando E, Hildebrand E et al (2013) Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh. Front Microbiol 3:445. CrossRefPubMedPubMedCentralGoogle Scholar
  172. Pennings SC, Grant M-B, Bertness MD (2005) Plant zonation in low-latitude salt marshes: disentangling the roles of flooding, salinity and competition. J Ecol 93:159–167CrossRefGoogle Scholar
  173. Piceno YM, Lovell CR (2000) Stability in natural bacterial communities: I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb Ecol 39:32–40PubMedCrossRefPubMedCentralGoogle Scholar
  174. Piceno YM, Noble PA, Lovell CR (1999) Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis. Microb Ecol 38:157–167PubMedCrossRefPubMedCentralGoogle Scholar
  175. Pomeroy LR, Darley WM, Dunn EL et al (1981) Primary production. In: Pomeroy LR, Wiegert RG (eds) The ecology of a salt marsh. Springer-Verlag, New YorkCrossRefGoogle Scholar
  176. Pott AS, Dahl C (1998) Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Microbiology 144:1881–1894PubMedCrossRefPubMedCentralGoogle Scholar
  177. Quillet L, Besaury L, Popova M et al (2012) Abundance, diversity and activity of sulfate-reducing prokaryotes in heavy metal-contaminated sediment from a salt marsh in the Medway Estuary, UK. Mar Biotechnol 14:363–381PubMedCrossRefPubMedCentralGoogle Scholar
  178. Ravit B, Ehrenfeld JG, Haggblom MM (2003) A comparison of sediment microbial communities associated with Phragmites australis and Spartina alterniflora in two brackish wetlands of New Jersey. Estuaries 26:465–474CrossRefGoogle Scholar
  179. Ravit B, Ehrenfeld JG, Haggblom MM et al (2007) The effects of drainage and nitrogen enrichment on Phragmites australis, Spartina alterniflora, and their root-associated microbial communities. Wetlands 27:915–927CrossRefGoogle Scholar
  180. Reboreda R, Caçador I (2007) Halophyte vegetation influences in salt marsh retention capacity for heavy metals. Environ Pollut 146(1):147–154Google Scholar
  181. Reboreda R, Caçador I (2008) Enzymatic activity in the rhizosphere of Spartina maritima: potential contribution for phytoremediation of metals. Mar Environ Res 65:77–84PubMedCrossRefPubMedCentralGoogle Scholar
  182. Reddy KR, Patrick WHJ, Lindau CW (1989) Nitrification-denitrification at the plant root-sediment interface in wetlands. Limnol Oceanogr 34:1004–1013CrossRefGoogle Scholar
  183. Reitl AJ, Overlander ME, Nyman AJ et al (2016) Microbial community composition and extracellular enzyme activities associated with Juncus roemerianus and Spartina alterniflora vegetated sediments in Louisiana saltmarshes. Microb Ecol 71:290–303CrossRefGoogle Scholar
  184. Rogers J, Harris J, Valiela I (1998) Interaction of nitrogen supply, sea level rise, and elevation on species form and composition of salt marsh plants. Biol Bull 195:235–237PubMedCrossRefPubMedCentralGoogle Scholar
  185. Rooney-Varga JN, Devereux R, Evans RS et al (1997) Seasonal changes in the relative abundance of uncultivated sulfate-reducing bacteria in a salt marsh sediment and the rhizosphere of Spartina alternaflora. Appl Environ Microbiol 63:3895–3901PubMedPubMedCentralGoogle Scholar
  186. Rozema J, Leendertse P, Bakker J et al (2000) Nitrogen and vegetation dynamics in European salt marshes. In: Weinstein MP, Kreeger DA (eds) Concepts and controversies in tidal marsh ecology. Springer, NetherlandsGoogle Scholar
  187. Schmid MC, Risgaard-Petersen N, van de Vossenberg J et al (2007) Anaerobic ammonium-oxidizing bacteria in marine environments: widespread occurrence but low diversity. Environ Microbiol 9:1478–1484CrossRefGoogle Scholar
  188. Schubauer JP, Hopkinson CS (1984) Above- and belowground emergent macrophyte production and turnover in a coastal marsh ecosystem, Georgia. Limnol Oceanogr 29:1052–1065CrossRefGoogle Scholar
  189. Seitzinger SP, Gardner WS, Spratt AK (1991) The effect of salinity on ammonium sorption in aquatic sediments: implications for benthic nutrient recycling. Estuaries 14:167–174CrossRefGoogle Scholar
  190. Shuang JL, Zhang XY, Zhao ZZ et al (2009) Bacterial phylogenetic diversity in a Spartina marsh in China. Ecol Eng 35:529–535CrossRefGoogle Scholar
  191. Smith JM, Green SJ, Kelley CA et al (2008) Shifts in methanogen community structure and function associated with long-term manipulation of sulfate and salinity in a hypersaline microbial mat. Environ Microbiol 10:386–394PubMedCrossRefPubMedCentralGoogle Scholar
  192. Su J, Ouyang W, Hong Y et al (2016) Responses of endophytic and rhizospheric bacterial communities of salt marsh plant (Spartina alterniflora) to polycyclic aromatic hydrocarbons contamination. J Soils Sediments 16:707–715CrossRefGoogle Scholar
  193. Sundby B, Vale C, Cacador I et al (1998) Metal-rich concentrations on the roots of salt marsh plants: mechanism and rate of formation. Limnol Oceanogr 43:245–252CrossRefGoogle Scholar
  194. Suntornvongsagul K, Burke DJ, Hamerlynk EP et al (2007) Fate and effects of heavy metals in salt marsh sediments. Environ Pollut 149:79–91PubMedCrossRefPubMedCentralGoogle Scholar
  195. Swarzenski CM, Doyle TW, Fry B et al (2008) Biogeochemical response of organic-rich freshwater marshes in the Louisiana delta plain to chronic river water influx. Biogeochemistry 90:49–63CrossRefGoogle Scholar
  196. Tabot PT, Adams JB (2013) Ecophysiology of salt marsh plants and predicted responses to climate change in South Africa. Ocean Coast Manag 80:89–99CrossRefGoogle Scholar
  197. Teal JM, Howes BL (2000) Salt marsh values: retrospection from the end of the century. In: Weinstein MP, Kreeger PA (eds) Concepts and controversies in tidal marsh ecology. Kluwer Academic Publishers, New York, pp 9–21Google Scholar
  198. Teal JM, Kanwisher J (1961) Gas exchange in a Georgia salt marsh. Limnol Oceanogr 6:388–399CrossRefGoogle Scholar
  199. Teal TH, Chapman M, Guillemette T et al (1996) Free-living spirochetes from Cape Cod microbial mats detected by electron microscopy. Microbiol SEM 12:571–584Google Scholar
  200. Tessier A, Campbell PG, Bisson M (1979) Sequential extraction procedure for the speciation of particulate trace metals. Anal Chem 51:844–851CrossRefGoogle Scholar
  201. Thomas F, Giblin AE, Cardon ZG et al (2014) Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments. Front Microbiol 5:309. CrossRefPubMedPubMedCentralGoogle Scholar
  202. Tobias CR, Macko SA, Anderson IC et al (2001) Tracking the fate of a high concentration groundwater nitrate plume through a fringing marsh: a combined groundwater tracer and in situ isotope enrichment study. Limnol Oceanogr 46:1977–1989CrossRefGoogle Scholar
  203. Tong C, Baustian JJ, Graham SA et al (2013) Salt marsh restoration with sediment-slurry application: Effects on benthic macroinvertebrates and associated soil-plant variables. Ecol Eng 51:151–160CrossRefGoogle Scholar
  204. Tremblay L, Benner R (2006) Microbial contributions to N-immobilization and organic matter preservation in decaying plant detritus. Geochim Cosmochim Acta 70:133–146CrossRefGoogle Scholar
  205. Treplin M, Pennings SC, Zimmer M (2013) Decomposition of leaf litter in a U.S. salt marsh is driven by dominant species, not species complementarity. Wetlands 33:83–89CrossRefGoogle Scholar
  206. Treusch AH, Leninger S, Kletzin A et al (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7:1985–1995PubMedCrossRefPubMedCentralGoogle Scholar
  207. Turner RE (2011) Beneath the salt marsh canopy: loss of soil strength with increasing nutrient loads. Estuar Coasts 34:1084–1093. CrossRefGoogle Scholar
  208. Turner RE, Howes BL, Teal JM et al (2009) Salt marshes and eutrophication: an unsustainable outcome. Limnol Oceanogr 54:1634–1642CrossRefGoogle Scholar
  209. Válega M, Lillebø AI, Pereira ME et al (2008) Long-term effects of mercury in a salt marsh: hysteresis in the distribution of vegetation following recovery from contamination. Chemosphere 71:765–772PubMedCrossRefPubMedCentralGoogle Scholar
  210. Valiela I (1995) Marine ecological processes, 2nd edn. Springer-Verlag, New YorkCrossRefGoogle Scholar
  211. Valiela I (2015) The Great Sippewissett salt marsh plots—some history, highlights, and contrails from a long-term study. Estuar Coasts 38:1099–1120CrossRefGoogle Scholar
  212. Valiela I, Bowen JL (2002) Nitrogen sources to watersheds and estuaries: role of land cover mosaics and losses within watersheds. Environ Pollut 118:239–248PubMedCrossRefPubMedCentralGoogle Scholar
  213. Valiela I, Cole ML (2002) Comparative evidence that salt marshes and mangroves may protect seagrass meadows from land-derived nitrogen loads. Ecosystems 5:92–102CrossRefGoogle Scholar
  214. Valiela I, Teal JM (1974) Nutrient limitation in salt marsh vegetation. In: Reimold RJ, Queen WH (eds) Ecology of halophytes. Academic Press, New YorkGoogle Scholar
  215. Valiela I, Teal JM, Sass W (1973) Nurient retention in salt marsh plots experimentally fertilized with sewage sludge. Estuar Coast Mar Sci 1:261–269CrossRefGoogle Scholar
  216. Valiela I, Teal JM, Cogswell C et al (1985) Some long-term consequences of sewage contamination in salt marsh ecosystems. In: Godfrey PJ, Kaynor ER, Pelczarski S, Benforado J (eds) Ecological considerations in wetlands treatment of municipal wastewaters. Van Nostrand Reinhold, New YorkGoogle Scholar
  217. Van Dyk JS, Pletschke BI (2012) A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes—Factors affecting enzymes, conversion and synergy. Biotechnol Adv 30:1458–1480PubMedCrossRefPubMedCentralGoogle Scholar
  218. Van Raalte CD, Valiela I, Carpenter EJ et al (1974) Inhibition of nitrogen fixation in salt marshes measured by acetylene reduction. Estuar Coast Mar Sci 2:301–305CrossRefGoogle Scholar
  219. Vieillard AM, Fulweiler RW (2012) Impacts of long-term fertilization on salt marsh tidal creek benthic nutrient and N2 gas fluxes. Mar Ecol Prog Ser 471:11–22CrossRefGoogle Scholar
  220. Vivanco L, Irvine I, Martiny JBH (2015) Nonlinear responses in salt marsh functioning to increased nitrogen addition. Ecology 96:936–947PubMedCrossRefPubMedCentralGoogle Scholar
  221. Wang M, Chen J-K, Bo L (2007) Characterization of bacterial community structure and diversity in rhizosphere soils of three plants in rapidly changing salt marshes using 16S rDNA. Pedosphere 17:545–556CrossRefGoogle Scholar
  222. Ward BB, Eveillard D, Kirshtein JD et al (2007) Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environ Microbiol 9:2522–2538PubMedCrossRefPubMedCentralGoogle Scholar
  223. Weber FH, Greenberg EP (1981) Rifampin as a selective agent for the enumeration and isolation of spirochetes from salt marsh habitats. Curr Microbiol 5:303–306CrossRefGoogle Scholar
  224. Weis JS, Weis P (2004) Metal uptake, transport and release by wetland plants: implications for phytoremediation and restoration. Environ Int 30:685–700PubMedCrossRefPubMedCentralGoogle Scholar
  225. Weis P, Windham L, Burke DJ et al (2002) Release into the environment of metals by two vascular salt marsh plants. Mar Environ Res 54:325–329PubMedCrossRefPubMedCentralGoogle Scholar
  226. Welsh A, Burke DJ, Hamerlynck EP et al (2010) Seasonal analyses of arbuscular mycorrrhizae, nitrogen-fixing bacteria and growth performance of the salt marsh grass Spartina patens. Plant Soil 330:251–266CrossRefGoogle Scholar
  227. Welsh A, Chee-Sanford JC, Connor LM et al (2014) Refined NrfA phylogeny improves PCR-based nrfA detection. Appl Environ Microbiol 80:2110–2119PubMedPubMedCentralCrossRefGoogle Scholar
  228. White DS, Howes BL (1994) Long-term 15N-nitrogen retention in vegetated sediments of a New England salt marsh. Limnol Oceanogr 39:1878–1892CrossRefGoogle Scholar
  229. Whiting GJ, Gandy EL, Yoch DC (1986) Photosynthesis in the salt marsh grass Spartina alterniflora and carbon dioxide enhancement of nitrogenase activity. Appl Environ Microbiol 52:108–113PubMedPubMedCentralGoogle Scholar
  230. Wigand C, McKinney RA, Chintala MM et al (2004) Denitrification enzyme activity of fringe salt marshes in New England (USA). J Environ Qual 33:1144–1151PubMedCrossRefPubMedCentralGoogle Scholar
  231. Wigand C, Brennan P, Stolt M et al (2009) Soil respiration rates in coastal marshes subject to increasing watershed nitrogen loads in southern New England, USA. Wetlands 29:952–963CrossRefGoogle Scholar
  232. Wilde P, Manal A, Stodden M et al (2009) Biodiversity of arbuscular mycorrhizal fungi in roots and soils of two salt marshes. Environ Microbiol 11:1548–1561PubMedCrossRefPubMedCentralGoogle Scholar
  233. Williams TP, Bubb JM, Lester JN (1994) Metal accumulation within salt marsh environments: a review. Mar Pollut Bull 28(5):277–290CrossRefGoogle Scholar
  234. Wilson AM, Evans T, Moore W et al (2015) Groundwater controls ecological zonation of salt marsh macrophytes. Ecology 96:840–849PubMedCrossRefPubMedCentralGoogle Scholar
  235. Xia J, Wan S (2008) Global response patterns of terrestrial plant species to nitrogen addition. New Phytol 179:428–439PubMedCrossRefPubMedCentralGoogle Scholar
  236. Yoch DC, Whiting GJ (1986) Evidence for NH4 + switch-off regulation of nitrogenase activity by bacteria in salt marsh sediments and roots of the grass Spartina alterniflora. Appl Environ Microbiol 51:143–149PubMedPubMedCentralGoogle Scholar
  237. Zehr JP, McReynolds LA (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium spp. Appl Environ Microbiol 55:2522–2526PubMedPubMedCentralGoogle Scholar
  238. Zehr JP, Jenkins BD, Short SM et al (2003) Nitrogenase gene diversity and microbial community structure: a cross system comparison. Environ Microbiol 5:539–554PubMedCrossRefPubMedCentralGoogle Scholar
  239. Zeleke J, Sheng Q, Wang J-G et al (2013) Effects of Spartina alterniflora invasion on the communities of methanogens and sulfate-reducing bacteria in estuarine marsh sediments. Front Microbiol 4:243. CrossRefPubMedPubMedCentralGoogle Scholar
  240. Zhang Y, Ding Y, Cai Z et al (2010) Response of methane emission to invasion of Spartina alterniflora and exogenous N deposition in the coastal salt marsh. Atmos Environ 44:4588–4594CrossRefGoogle Scholar
  241. Zhang QF, Peng JJ, Chen Q et al (2011) Impacts of Spartina alterniflora invasion on abundance and composition of ammonia oxidizers in estuarine sediment. J Soil Sediment 11:1020–1030CrossRefGoogle Scholar
  242. Zhang Q, Peng J, Chen Q et al (2013) Abundance and composition of denitrifiers in response to Spartina alterniflora invasion in estuarine sediment. Can J Microbiol 59:825–836PubMedCrossRefPubMedCentralGoogle Scholar
  243. Zimmer M, Pennings S, Buck TL et al (2004) Salt marsh litter and detritivores: a closer look at redundancy. Estuaries 27:753–769CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Biology DepartmentAdelphi UniversityGarden CityUSA

Personalised recommendations